Aquaculture has been the world’s fastest-growing sector for food production and contributes significantly to rural development and food security in many countries. Despite its proliferation, the uncertainties in aquaculture have not been well addressed. In this paper, we developed a stochastic simulation model to explore the effects of risky economic and biological variables on the profitability of shrimp aquaculture. The profitability is measured with the probability distribution of net present value of the aquaculture production. In the base scenario, we examined the effects of risks in disease, random shocks, and biological growth on the profitability. In the second fold, we modelled the different levels of vertical integration by adding input and output price uncertainties to the simulations. In the last scenario, we were interested in how different social and institutional risks will impact the success of vertical integration. Specifically, we investigated how uncertainties in land rights and international trade interact with various vertical integration profiles. Our results contribute to further understanding of the risk profiles of shrimp aquaculture and how social and institutional issues constrain the industry and rural development.